I really would be dissapointed if your theory came to be correct. What happened in this episode seemed to be a really good and needed gamechanger. The series needs to change tracks, and I think It would be a genious move to use the attention generated by the Movie to give the series a new boost and try new things.
After watching it I started thinking about Alias, and how they suddenly changed all the status quo, dismantling SD-6
SHIELD's not going to be as monolithic as it was, but it's still going to be around in some form as Natasha's blithely waltzing out of the congressional hearing indicates. Even if that form eventually turns out to be HAMMER.
The Uprising story arc has been pretty good, but that's because it's been worked out in conjunction with CA:TWS
-- the initial Dark World
tie in was so inconsequential it could easily have been the series opener, though the 2nd one where they brought in Sif as a guest star certainly redeemed things.
I really do want Ward to be an irredeemable traitor or at least found to be a martyr to the cause after being fatally shot in the face, but based on the first half of the season I'm not certain the writers have what it takes to go there, nor the rage-inducing stupidity to fridge Hand as a vehicle for Ward's manpain. With Hill taking up a job at Stark Industries and thus removing herself from the post-Fury directorship fubar the comics landed her with, Hand has the right sort of ruthlessly pragmatic attitude to traitors that SHIELD needs right now.